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• We studied flocculation of microalgae- and clay-containing suspensions. • Investigations were done in different microalgal growth phases. • A two-class flocculation kinetic model and Bayesian calibration were applied. • Effect of organic matter secreted by algae on flocculation kinetics was evaluated. • Distinct flocculation mechanisms were identified in different microalgal growth phases. Interplays between microalgae and clay minerals enhance biologically mediated flocculation, thereby affecting the sedimentation and transportation of suspended particulate matter (SPM) in water and benthic environments. This interaction forms larger flocs with a higher settling velocity and enhances SPM sinking. The aim of this study was to investigate the flocculation kinetics of microalgae and clay in suspension and to elucidate the mechanisms associated with such interactions. Standard jar test experiments were conducted using various mixtures of kaolinite and microalgal samples from batch cultures (Chlorella vulgaris) to estimate biologically mediated flocculation kinetics. The organic matter (OM) composition secreted by the microalgae was characterized using a liquid chromatography - organic carbon detection system, and quantitative analysis of transparent exopolymer particles was conducted separately. A two-class flocculation kinetic model, based on the interaction between flocculi and flocs, was also adopted to quantitatively analyze the experimental data from flocculation. Results from the flocculation kinetic tests and OM analyses, in association with other data analyses (i.e., floc size distribution and flocculation kinetic model), showed that flocculation increased with OM concentration during the growth phase (10–20 d). However, on day 23 during the early stationary phase, flocculation kinetics started decreasing and substantially declined on day 30, even though the amount of OM (mainly biopolymers) continued to increase. Our results indicate that an adequate quantity of biopolymers produced by the microalgal cells in the growth phase enhanced floc-to-floc attachment and hence flocculation kinetics. In contrast, an excessive quantity of biopolymers and humic substances in the stationary phase enhanced the formation of polymeric backbone structures and flocculation via scavenging particles but simultaneously increased steric stabilization with the production of a large number of fragmented particles. [Display omitted] [ABSTRACT FROM AUTHOR]